This is another sad example of the US's twisted immigration policy. Brilliant entrepreneurs, scientists, and academics want to come in legally and are rejected, while thousands of others come in illegally.
I definitely agree that the US immigration system is pretty broken, but assuming that the US system was fixed, and there were still different kinds of visas, it wouldn't magically be broken again because people got denied for applying for the wrong kind.
PG has written about this idea here: http://www.paulgraham.com/foundervisa.html
And actually, your point illustrates quite effectively why there is illegal immigration. If the system is broken, people will try to work around it, rather than through it. Bureaucracy for the lose.